Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.

        Anonymize samples off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.

        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.27.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-06-24, 19:50 CDT based on data in: /project/xinhe/xsun/camseq/data_multicelltypes/merged_workspace/reports_all

        General Statistics

        Showing 20/20 rows and 4/4 columns.
        Sample NameUnique ReadsPass Dedup% AlignedTrimmed bases
        S1.genome
        46.4M
        63.4%
        98.9%
        36.9%
        S2.genome
        61.0M
        68.4%
        99.2%
        40.9%
        S3.genome
        81.4M
        59.0%
        99.1%
        38.0%
        S4.genome
        62.9M
        57.1%
        99.0%
        36.1%
        S5.genome
        73.2M
        62.9%
        99.1%
        37.9%
        S6.genome
        32.4M
        38.4%
        98.8%
        37.3%
        S7.genome
        58.6M
        60.9%
        99.0%
        34.9%
        S8.genome
        55.3M
        77.8%
        99.0%
        37.8%
        S9.genome
        57.2M
        74.5%
        98.9%
        37.0%
        S10.genome
        56.0M
        74.8%
        99.0%
        37.3%
        S11.genome
        17.2M
        23.9%
        29.0%
        71.4%
        S12.genome
        22.2M
        33.4%
        26.0%
        68.5%
        S13.genome
        17.2M
        26.7%
        28.6%
        71.4%
        S14.genome
        26.4M
        31.0%
        28.5%
        71.1%
        S15.genome
        19.0M
        29.4%
        25.8%
        69.3%
        S16.genome
        9.8M
        53.1%
        23.8%
        80.7%
        S17.genome
        27.3M
        25.0%
        30.8%
        72.6%
        S18.genome
        12.4M
        18.4%
        27.3%
        69.2%
        S19.genome
        9.7M
        16.2%
        26.1%
        69.8%
        S20.genome
        18.3M
        34.4%
        26.5%
        69.9%

        UMICollapse

        Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.URL: https://github.com/Daniel-Liu-c0deb0t/UMICollapseDOI: 10.7717/peerj.8275

        Deduplicated Reads

        Created with MultiQC

        UMI Stats

        Statistics from running umicollapse

        • Positions Dedup: Total number of positions deduplicated
        • Mean #UMI: Mean number of unique UMIs per position
        • Max #UMI: Max number of unique UMIs per position
        • Discarded reads: Discarded unmapped, unpaired, or chimeric reads
        Created with MultiQC

        HISAT2

        Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        Created with MultiQC

        Cutadapt

        Version: 4.9

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Cutadapt4.9

        MultiQC v1.27.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.